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Does anyone know what genes produce the longest mRNAs? I am planning a project on synthetic introns and want to use stuffer fragments to vary intron size. Obviously they must not contain any splicing sites, hence I plan on buying cDNA clones.

It would be incredibly appreciated if someone could point fingers at transcripts that are 12...20 kbp long (and ideally have no other known isoforms or cryptic splicing sites).

Thank you!

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    $\begingroup$ In which organism? BTW, since you're ordering cDNA anyway, I imagine most of the non-cryptic splice sizes will be gone anyway. $\endgroup$ – Devon Ryan May 3 '17 at 14:53
  • $\begingroup$ mammalian, prefferably mouse $\endgroup$ – Ooooo May 8 '17 at 13:06
  • $\begingroup$ Do you mean "longest transcript without introns"? if you want a gene with only a single isoform, I'd parse the latest mouse gtf, and look for genes with only a single transcript line. You can get the gene length (though oddly enough, not the transcript length) in there too. $\endgroup$ – swbarnes2 May 8 '17 at 18:38
  • $\begingroup$ These question here is refering to the longest cDNAs. No matter if they contained introns before. The final product mustr not contain any splicing sites $\endgroup$ – Ooooo May 8 '17 at 23:18
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To R!

  1. Download the most comprehensive GTF file from Gencode for mouse.
  2. Do the following in R (I'll put comments in the code so you can hopefully follow along):
library(GenomicFeatures)

#Load the GTF file and make a TxDb object
txdb = makeTxDbFromGFF("gencode.vM13.annotation.gtf", format="gtf")

#Make a GRangesList, with transcripts split per gene
grl = transcriptsBy(txdb, by="gene")

# Filter the GRangesList for genes with one annotated isoform
grl2 = grl[which(elementNROWS(grl) == 1)]

# Make a new GRangesList of the exons per gene from above
grl = exonsBy(txdb, by="gene")
grl = grl[which(names(grl) %in% singleIsoformGenes)]

# Get the length of each single-isoform gene
lens = sum(width(grl))

# Get the top 10 single isoform genes by length
head(lens[order(lens, decreasing=T)], n=10)

You then get the following output, with gene IDs on top and lengths below that:

ENSMUSG00000020255.8 ENSMUSG00000101609.1 ENSMUSG00000104211.1 
              123179                84395                74456 
ENSMUSG00000109536.1 ENSMUSG00000109125.1 ENSMUSG00000047888.9 
               30942                25241                17327 
ENSMUSG00000022262.7 ENSMUSG00000066108.7 ENSMUSG00000033826.9 
               15630                14964                14583 
ENSMUSG00000032855.5 
               14170 
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